reordXlist: Reorders Design Matrices

Description

Reorders design matrices so excluded parents appear last, and high probability parents appear first, thus increasing computational efficiency.

Usage

reordXlist(X.list, marker.type="MSW")

Arguments

X.list

list of design matrices for each offspring derived using getXlist. Mismatch information must be present (see mismatches)

marker.type

"MSW" or "MSC" for co-dominant markers with Wang's (2004) model of genotyping error or CERVUS's model of genotyping error (Kalinowski, 2006; Marshall, 1998) or "AFLP" for dominant markers (Hadfield, 2009).

Value

X.list for which parents are reordered

Details

The design matrices are reordered by the number of mismatches between a parent and offspring for codominant markers, and by the probability of the offspring genotype conditional on parent genotype for dominant markers.

Examples

Run this code

# NOT RUN {
data(WarblerG)
A<-extractA(WarblerG)

ped<-matrix(NA, 5,3)
ped[,1]<-1:5
ped[,2]<-c(rep(NA, 4), 3)
ped[,3]<-c(rep(NA, 4), 4)

genotypes<-simgenotypes(A, ped=ped)

sex<-c("Female", "Male", "Female", "Male","Female")
offspring<-c(0,0,0,0,1)

data<-data.frame(id=ped[,1], sex, offspring)

var1<-expression(varPed(x="offspring", restrict=0))
PdP<-PdataPed(formula=list(var1), data=data)

X.list<-getXlist(PdP)
# creates design matrices for offspring (in this case indivdiual "5")

X.list<-mismatches(X.list, G=genotypes$Gobs)
X.list<-fillX.G(X.list, A=A, G=genotypes$Gobs)

X.list.reord<-reordXlist(X.list)

# The design matrices for the genetic likelihoods are reordered
# by the number of mismatches.  The true parental combination
# now appears first rather than last.

X.list$X$"5"$G
X.list.reord$X$"5"$G
# }